The Discovery of 7-Methyl-2-[(7-methyl[1,2,4]triazolo[1,5- a]pyridin-6-yl)amino]-9-(tetrahydro-2 H-pyran-4-yl)-7,9-dihydro-8 H-purin-8-one (AZD7648), a Potent and Selective DNA-Dependent Protein Kinase (DNA-PK) Inhibitor

Article abstract of DOI:10.1021/acs.jmedchem.9b01684

DNA-PK is a key component within the DNA damage response, as it is responsible for recognizing and repairing double-strand DNA breaks (DSBs) via non-homologous end joining. Historically it has been challenging to identify inhibitors of the DNA-PK catalyti

Full text of DOI:10.1021/acs.jmedchem.9b01684

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Drug Annotation
The discovery of 7-methyl-2-[(7-methyl[1,2,4]triazolo[1,5-a]pyridin-6-
yl)amino]-9-(tetrahydro-2H-pyran-4-yl)-7,9-dihydro-8H-purin-8-one (AZD7648),
a potent and selective DNA-dependent protein kinase (DNA-PK) inhibitor
Frederick Woolf Goldberg, M. Raymond V. Finlay, Attilla Ting, David Beattie, Gillian Lamont, Charlene
Fallan, Gail Wrigley, Marianne Schimpl, Martin R. Howard, Beth Williamson, Mercedes Vazquez-
Chantada, Derek Barratt, Barry Davies, Elaine Cadogan, Antonio Ramos Montoya, and Emma Dean
J. Med. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jmedchem.9b01684 • Publication Date (Web): 18 Dec 2019
Downloaded from pubs.acs.org on December 18, 2019
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Journal of Medicinal Chemistry
The discovery of 7-methyl-2-[(7-methyl[1,2,4]triazolo[1,5-a]pyridin-6-yl)amino]-9-(tetrahydro-2H-
pyran-4-yl)-7,9-dihydro-8H-purin-8-one (AZD7648), a potent and selective DNA-dependent
protein kinase (DNA-PK) inhibitor
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Frederick W. Goldberg,*1 M. Raymond V. Finlay,1 Attilla K. T. Ting,1 David Beattie,1 Gillian M.
Lamont,1 Charlene Fallan,1 Gail L. Wrigley,1 Marianne Schimpl,2 Martin R. Howard,1 Beth Williamson,1
Mercedes Vazquez-Chantada,2 Derek G. Barratt,2 Barry R. Davies,1 Elaine B. Cadogan,1 Antonio Ramos-
Montoya,1 Emma Dean1
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1 Oncology R&D, AstraZeneca, Cambridge, UK
2 Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
KEYWORDS
DNA-PK; AZD7648; DDR; kinase; permeability; selectivity; PIKK; oncology; cancer; PARP; olaparib.
ABSTRACT
DNA-PK is a key component within the DNA damage response, as it is responsible for recognizing and
repairing double-strand DNA breaks (DSBs) via non-homologous end joining. Historically it has been
challenging to identify inhibitors of the DNA-PK catalytic subunit (DNA-PKcs) with good selectivity
versus the structurally related PI3 (lipid) and PI3K-related protein kinases. We screened our corporate
collection for DNA-PKcs inhibitors with good PI3 kinase selectivity, identifying compound 1.
Optimization focused on further improving selectivity while improving physical and pharmacokinetic
properties, notably co-optimization of permeability and metabolic stability, to identify compound 16
(AZD7648). Compound 16 had no significant off-target activity in the protein kinome, and only weak
activity versus PI3Kα/γ lipid kinases. Monotherapy activity in murine xenograft models was observed,
and regressions were observed when combined with inducers of DSBs (doxorubicin or irradiation) or
PARP inhibition (olaparib). These data support progression into clinical studies (NCT03907969).
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Introduction
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Genomic instability is a characteristic of tumor cells, as it enables the mutagenesis required for tumor
progression and has been described as underpinning the classical hallmarks of cancer.1 The detection and
repair of DNA damage by the DNA damage response (DDR)2 is important for cancer cells to manage
their inherent genomic instability. Furthermore, many cancers have acquired DDR mutations or
deficiencies that can render the cancer cell more susceptible to pharmacological inhibition of the
remaining functional components of DNA repair.3–5 DNA-dependent protein kinase (DNA-PK) is a key
node within the DDR, as it is responsible for recognizing and repairing double-strand DNA breaks (DSBs)
via non-homologous end joining (NHEJ),6 a common repair process for DSBs which are the most
cytotoxic form of DNA damage.
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DNA-PK is a complex composed of a catalytic (kinase) subunit DNA-PKcs and the Ku70/80 heterodimer
which initially recognizes the DSB and recruits the kinase subunit. DNA-PKcs can phosphorylate a
variety of substrates known to be important for NHEJ that include Artemis, x-ray repair cross-
complementing protein 4 (XRCC4) and XRCC4-like factor (XLF), and the autophosphorylation of DNA-
PKcs is important for DNA end processing and accessibility. In addition to its role in NHEJ, DNA-PKcs
is also known to be important for other cellular processes,7 as it can phosphorylate a number of other
substrates including replication protein A 32 kDa subunit (RPA32) and H2A histone family member X
(H2AX).8 Given the importance of DNA-PK for NHEJ repair, DNA-PKcs inhibitors may have clinical
utility for oncology by combining with DSB inducers such as radiation or inhibitors of topoisomerase II
such as doxorubicin. We were also interested in exploring the efficacy in preclinical species for a selective
DNA-PKcs inhibitor as monotherapy, particularly in cell lines with deficiencies in other DDR targets
notably ataxia-telangiectasia mutated kinase (ATM), and/or in combination with other DDR inhibitors
such as olaparib, an inhibitor of poly ADP-ribose polymerase (PARP).
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The ability to explore multiple combination hypotheses, preclinically and clinically, in part influenced
our strategy to target a clinical candidate with excellent kinome selectivity, pharmacokinetic properties
that would allow us to target either continuous or intermittent dosing in the clinic, and no predicted issues
with drug-drug interactions. Historically it has been challenging to identify inhibitors of DNA-PKcs that
have good selectivity versus the structurally related PI3 lipid kinases (PI3Kα, β, δ, γ)9 and the PI3K-
related protein kinase (PIKK) family which includes kinases that are also key DDR targets such as ataxia
telangiectasia mutated and Rad3-related (ATR) and ATM.10,11 Optimization of a previous DNA-PKcs
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inhibitor series had identified KU60648,12 which was not progressed due to the toxicity profile in
rats.13 We hypothesized that PI3 kinase off-target activity may have contributed to this toxicity, for
example due to the reported role of PI3Kα in cardioprotection,14 highlighting the importance of high
kinome selectivity. Selectivity was therefore a key factor when designing our screening cascade and
was a focus of the subsequent optimization.
Results and Discussion
We performed a high throughput screen of ~500k compounds from the AstraZeneca corporate collection,
with the aim of identifying DNA-PKcs inhibitors that had selectivity versus PI3Kα by simultaneously
screening compounds against both targets. This work identified hit compound 1 (Table 1), which had
good DNA-PKcs potency and good biochemical selectivity versus the PI3 kinases (supplemental
information). Compounds with the 7,9-dihydro-8H-purin-8-one bicyclic core structure have previously
been reported as inhibitors of dual-specificity protein kinase (TTK).15 Compound 1 was screened against
a selectivity panel at Thermofisher’s SelectScreen Kinase Profiling Service (details in supplemental), and
gave generally good selectivity versus the protein kinome, but with notable activity versus TTK
(pIC50=7.7), and colony stimulating factor 1 receptor (CSF1R, pIC50=7.6). Compound 1 was lipophilic
(logD7.4=3.7) and had poor associated physical properties, so our initial focus was to vary the cyclopentyl
group, which was thought to be oriented into the ribose pocket, to improve potency and reduce logD.
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Replacement of the cyclopentyl 1 with a phenyl group 2 reduced potency (Table 1), albeit with a
significant decrease to measured logD7.4 (4.1 to 2.8), a greater decrease than you would expect for an
isolated cyclohexyl to phenyl change presumably due to conjugation of the purinone nitrogen to the
phenyl ring. Expansion of the cyclopentyl to cyclohexyl analogue 3 gave a small increase in potency.
Addition of a hydroxyl group into the para position of the cyclohexyl to give 4 provided a compound with
good biochemical and cell potency in a suitable logD range (logD7.4=2.3), and was thus used as the starting
point for further optimization. Removal of the N-Methyl group to give 5 reduced potency, despite having
no impact on lipophilicity.
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Table 1. Initial screening hit 1 and variations to the cyclopentyl group to improve potency and reduce
lipophilicity.
O
R2
N
N
OMe
R1
N
N
H
N
Example
R1
R2
DNA-PKcs
DNA-PKcs logD7.4
a
b
enzyme pIC50 cell pIC50
1
2
3
4
5
Me
Me
Me
Me
H
Cyclopentyl
8.3
7.9
8.6
9.5
8.7
6.5
-
3.7
2.8
4.1
2.3
2.3
Phenyl
Cyclohexyl
6.4
7.5
6.8
Trans-4-hydroxycyclohexyl
Trans-4-hydroxycyclohexyl
a Measured by time resolved fluorescence, arithmetic mean of n≥3. Standard error of the mean (SEM) values are listed in the
supporting information, and are all <0.15.
b
Inhibition of autophosphorylation (S2056) induced by irradiation in A549 cells by ELISA, arithmetic mean of n≥3. SEM
values are listed in the supporting information, and are all <0.16.
Compound 4 had retained the off-target activities versus TTK (pIC50 = 7.4) and CSF1R (pIC50 = 7.9),
along with some PI3 kinase activities, and we were interested to investigate the binding mode of this
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compound to guide further optimization. We were unable to generate a crystal structure of DNA-PKcs
due to technical challenges with this very large protein,16 but we were able to exploit crystal structures of
4 bound to CSF1R and PI3Kγ. These structures confirmed that 4 could adopt different binding modes. In
CSF1R (Figure 1a), the 4-methoxy-2-methylaniline flipped out of the ATP pocket, lying along the solvent
exposed channel, where the aniline NH undergoes a hydrogen bond with the main chain C=O of Cys666.
The crystal structure with PI3Kγ (Figure 1b) is more likely to be representative of the binding mode to
DNA-PKcs given the close structural homology, and in the PI3Kγ structure the aniline was bound the
other way around (into the pocket), with the aniline NH hydrogen bonded to Glu880. A DNA-PKcs
homology model was built based on the PI3Kγ crystal structure to guide design. We were interested to
see if we could optimize the aniline to retain the assumed DNA-PKcs binding mode, removing the
possibility of the alternative binding mode and thereby remove CSF1R and TTK activity.17
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Figure 1. Crystal structures of 4 in (a) CSF1R (PDB 6T2W) and (b) PI3Kγ (PDB 6T3B), with different
observed binding modes. The protein orientation presented throughout the paper are with N-lobe
(featuring a β-sheet with five strands) to the top, C-lobe at the bottom with hinge to the left. The binding
mode of 4 in DNA-PKcs is unknown but is likely to be better modelled by the PI3Kγ structure given the
close structural homology between DNA-PKcs and PI3Kγ. Amino acids in the hinge region are depicted
as sticks: Cys666 for CSF1R (left); Glu880 and Val882 for PI3Kγ (right).
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Page 6 of 35
Despite the moderate logD of compound 4, it was rapidly metabolized by human microsomes (CLint = 49
µl/min/mg). In addition, the para-methoxy aniline motif was considered a potential reactive metabolite
liability, as there was evidence (supplementary information) to suggest this could generate a reactive
iminoquinone18,19 via dealkylation of the methoxy group and subsequent oxidation. While probing the
structure-activity relationship (SAR) of the aniline group (Table 2) we focused on identifying potent
groups with good ligand lipophilic efficiency (LLE or LipE, pIC50-logD)20,21 that did not possess a labile
aromatic methoxy group. Removal of the para-methoxy 6 or the ortho-methyl 7, or removing both to give
compound 8, all substantially reduced potency, as did moving the para-methoxy into the meta position 9.
From the DNA-PKcs homology model, the para-methoxy group was expected to bind near several polar
groups, including Lys3753 within hydrogen bonding distance (see Figure 2c). Consequently, we focused
on identifying alternative groups that could theoretically mimic the methoxy by placing a hydrogen bond
acceptor into the para position. Notably, we found that an imidazopyridine that places an aromatic
nitrogen into the para position 10 had promising potency, considering it is missing the important ortho
methyl group. The ortho methyl was added into both positions 11 and 12, which confirmed a significant
boost in potency for 12 (but not 11). As we knew from previous SAR (for example comparing 9 to 6) a
hydrogen bond acceptor could be tolerated in the meta position, and we were interested in trying to reduce
the basicity of the imidazopyridine (vide infra), we synthesized triazolopyridine 13. This change was well
tolerated so we synthesized the corresponding ortho methyl 14, which had particularly impressive
potency. The ortho methyl on the aniline group gave a >10x increase in biochemical potency (>1 log unit)
across four matched pairs (cf. 4, 6, 12, 14 to 7, 8, 10, 13), while maintaining or reducing logD, and thus
could be described as a “magic methyl”.22 This striking increase in potency suggests that, in addition to
making an effective lipophilic interaction in the hydrophobic pocket consisting of Tyr3791, Leu3806 and
Ile3940 (see Figure 2d), the methyl may also confer a beneficial conformational effect, by favoring a
bioactive conformation where there is a twist between the aromatic amine and the purinone core.
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Table 2. Variations to the aniline.
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OH
1
2
3
4
O
N
N
N
5
6
R
N
H
N
7
8
9
Example R
DNA-PKcs
DNA-PKcs logD7.
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a
b
enzyme pIC50 cell pIC50
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OMe
4
9.5
7.5
2.3
6
7
8.0
8.0
6.6c
5.9c
2.5
2.3
OMe
8
9
6.9
8.5
5.3c
6.9c
2.4
2.6
OMe
10
11
8.1c
8.3
-
1.8
1.2
N
N
N
N
5.7c
N
N
12
13
9.6
8.2
6.6
-
1.4
1.7
N
N
N
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N
14
10.1
7.3
1.3
N
N
1
2
3
4
5
6
7
a Measured by time resolved fluorescence, arithmetic mean of n≥3. SEM values are listed in the supporting information, and
are all <0.15.
8
9
b Inhibition of autophosphorylation (S2056) induced by irradiation in A549 cells by ELISA. Arithmetic mean of n≥3 unless
otherwise stated. SEM values are listed in the supporting information, and are all <0.15 for compounds with n≥3.
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c n=1.
Compound 12 had excellent biochemical potency, particularly considering the very low lipophilicity
(logD7.4=1.4). However, there was a larger drop-off in potency between biochemical and cell potency
than we typically observe, which was presumed to be due to poor cell permeability and/or efflux. A549
cells express the efflux transporters breast cancer resistance protein (BCRP), multi-drug resistant protein
1 (MRP1) and to a lesser extent P-glycoprotein (P-gp)23 which can increase the difference in potency
observed in biochemical and cellular assays. We later observed that compound 12 had a high efflux ratio
(ER) in a Caco-2 assay (Papp A to B = 0.4 x 10-6 cm/s, ER 66), and the intrinsic Caco-2 permeability was
poor even in the presence of efflux inhibitors (Papp,int A to B = 1.6 x 10-6 cm/s), consistent with the
hypothesis that the A549 cell potency was compromised by poor permeability and/or efflux.
While improvements in permeability can often be achieved by increasing the lipophilicity,24,25 we chose
to maintain the low logD of compound 12 and to instead address permeability with structural changes,
with the aim that this would result in a compound that could combine permeability with favorable
properties associated with lower lipophilicity such as solubility and metabolic stability. We first targeted
the basicity of the nitrogen in the imidazopyridine ring, by addition of an extra nitrogen26 as described
above to give triazolopyridine 14 (Table 3), as this change was predicted to substantially reduce the
basicity. Despite nominally increased polar surface area, the lipophilicity did not change, and the intrinsic
permeability as measured in a Caco-2 assay with additional efflux inhibitors27 improved, although efflux
ratio in a conventional Caco-2 ABBA assay28 remained unchanged. Another productive change was to
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remove the donor in the ribose group, by conversion of the trans-4-hydroxycyclohexyl to a 4-
tetrahydropyran. While the biochemical potency did not increase from 12 to 15, cell potency did increase
suggesting an improvement in cell permeability. Both Caco-2 intrinsic permeability and efflux ratio were
improved by this change, however some efflux was still observed and the weak base apparently
contributed to some hERG activity.29 Combining both structural changes (triazolopyridine and
tetrahydropyran) gave compound 16, which combined good cell potency with excellent intrinsic
permeability, no efflux, and reduced hERG potency. Measured pKa values (of the conjugate acid)
confirmed that triazolopyridine 16 (pKa = 3.4) is significantly less basic than imidazopyridine 15 (pKa =
7.1).
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
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20
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An alternative approach taken was the addition of a methyl alpha to the hydroxy as in compounds 17 and
18. Compound 17 (logD7.4=1.1) retains good enzyme and cell potency, however Caco-2 data confirmed
that this compound still had high efflux (efflux ratio = 27). Switching to cis isomer 18 gave a notable and
surprising increase in lipophilicity (logD7.4=1.9), and had excellent permeability and no efflux. Other
approaches to removing the donor were tried, for example removal of the hydroxy to give cyclohexyl 19.
This gave a compound with high permeability and no efflux, but presumably due to the higher
lipophilicity, and potentially the availability of an unsubstituted cycloalkyl group for metabolism,
compound 19 gave very high metabolism in a human microsome assay (CLint = 93 µl/min/mg).
Lipophilicity was substantially reduced by bis-fluorination to give 20 which retained good intrinsic
permeability and low efflux, but human microsome stability remained poor (CLint = 68 µl/min/mg) so 20
was not suitable for further progression. Consequently compounds 16 and 18 were selected for further
profiling, and 16 was ultimately nominated as clinical candidate AZD7648.
Table 3. Modulating permeability and efflux by reducing basicity and masking polarity.
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O
N
R1
N
1
2
3
N
R2
4
5
N
H
N
6
7
8
9
Ex. R1
R2
DNA-
PKcs
DNA-
logD7.4 pKac Papp,int
A
Papp A to ABBA hERG
PKcs cell
to B x 10-6 B x 10-6
efflux
ratiof
66
IC50
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
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a
b
pIC50
pIC50
cm/sd
cm/se
(µM)
OH
12
9.6
6.6
1.4
1.6
0.4
N
N
N
[
[
OH
14
10.1
9.4
9.2
9.5
9.4
9.8
9.7
7.3
7.3
7.0
6.9
7.2
7.6
7.3
1.3
1.5
1.3
1.1
1.9
3.1
2.0
7.5
21
69
11
49
50
38
0.4
11
22
0.7
24
24
23
98
N
N
[
[
[
[
[
[
[
[
O
15
7.1
3.4
3.1
1.2
27
8.1
N
N
N
N
N
N
N
[
N
O
16
>198
N
[
N
17
OH
N
[
OH
N
18
3.6
1.2
0.5
0.9
>198
N
[
N
19
N
[
F
N
20
N
F
[
a Measured by time resolved fluorescence, arithmetic mean of n≥3. SEM values are listed in the supporting information, and
are all <0.15.
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b Inhibition of autophosphorylation (S2056) induced by irradiation in A549 cells by ELISA. Arithmetic mean of n≥3 unless
otherwise stated. SEM values are listed in the supporting information, and are all <0.15.
1
2
3
c Measured pKa of the conjugate acid. The pKa value for 15 is assumed to be measuring the protonated imidazopyridine. The
pKa values for 16 and 18 may be measuring either the protonated triazolopyridine or pyrimidine core.
d Intrinsic permeability as measured by Caco-2 in the presence of efflux inhibitors. The intrinsic Caco-2 permeability assay is
used within AstraZeneca following in-house analysis that a concentration dependent permeability is observed for efflux
transporter substrates.27
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e Permeability as measured in a conventional Caco-2 ABBA assay (without efflux inhibitors).28
f Efflux ratios throughout the article have been calculated from Papp B to A / Papp A to B.
Compound 16 was potent in both biochemical and cell assays despite having low molecular weight (380
Da) and moderate lipophilicity (logD7.4=1.3). This optimized structure combined potency with good
permeability, crystalline solubility and metabolic stability. Compound 16 also had favorable
pharmacokinetic properties in preclinical species (Table 4), with low clearance and high oral
bioavailability in rat, and moderate clearance and high bioavailability in dog. Clearance was primarily
metabolic, although as often observed with moderately polar molecules30 some renal clearance of parent
was observed with IV dosing (10% in rat at 2 mg/kg, 1.1% in dog at 1 mg/kg). The volume of distribution
was moderate in both species (Vss = 1.4 in rat, 0.7 in dog); as expected for a neutral compound with
moderate lipophilicity.31 Compound 16 had excellent metabolic stability in vitro in human hepatocytes
(CLint = 0.5 µl/min/106 cells), and low protein binding (76% fraction unbound in human plasma), although
protein binding was not a parameter that we had actively optimised.32 Due to the presence of aromatic
azaheterocycles, and in particular the triazolopyridine which has an unsubstituted carbon adjacent to two
sp2 nitrogens, we were concerned about the possibility of aldehyde oxidase (AO) metabolism,33 that may
not be observed in a standard human hepatocyte incubation but could nevertheless be an issue in vivo.
However, no AO metabolism was observed in a human cytosol assay with and without an AO inhibitor.
In human, compound 16 is predicted to have a moderate half-life of ~5 hours from these data. In a panel
of recombinant CYP enzymes the metabolism of AZD7648 was mediated predominantly by CYP3A4 and
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CYP3A5. No significant inhibition (>30 µM IC50), time-dependent inhibition (<20% shift) or induction
(<20% of control) of CYP enzymes was observed in vitro, so the risk of drug-drug interactions via these
enzymes was considered to be low.
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8
9
Table 4. Potency, physical and pharmacokinetic properties for 16.
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Assay
Data
DNA-PKcs enzyme IC50 (nM)a
0.6
pDNA-PKcs (S2056) A549 cell IC50 (nM)b
91
Physical form by X-ray powder diffraction (XRPD) Crystalline
Solubility FaSSIF pH 6.5 (µM)c
180
Solubility SGF pH 1.2 (µM)d
>10000
22
Permeability (Caco-2 Papp A to B x 10-6 cm/s)e
Efflux ratio (Caco-2 ABBA)e
1.2
Human, rat, dog plasma protein binding (% fu)f
76, 65, 79
0.5, <1.2, <1
Human, rat, dog hepatocyte CLint (µl/min/106 cells)
Rat, dog IV clearance (mL/min/kg)g
Rat, dog oral bioavailability F (%)g
29, 4.0
104, 93
a Measured by time resolved fluorescence, geometric mean of n=16. pIC50 SEM = 0.05.
b Inhibition of autophosphorylation (S2056) induced by irradiation in A549 cells by ELISA, geometric mean of n=13. pIC50
SEM = 0.08.
c Solubility of a crystalline sample (by XRPD) in fasted state simulated intestinal fluid (FaSSIF).
d Solubility of a crystalline sample (by XRPD) in simulated gastric fluid (SGF).
e Permeability and efflux ratio as measured by Caco-2 ABBA assay (without efflux inhibitors).
f There was no evidence of concentration dependent protein binding in any species; % fu data shown is average across range
of 0.03-100 µM drug concentration.
g Male Han Wistar rats or beagle dogs following a single administration of 16 by IV (2 mg/kg rat, 1 mg/kg dog) and PO (5
mg/kg rat, 2 mg/kg dog).
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Journal of Medicinal Chemistry
Kinome selectivity of compound 16 was assessed in Thermofisher’s SelectScreen Kinase Profiling
Service, where it was found to be highly selective versus the protein kinome, with measurable activity but
good selectivity ratios versus the PI3 (lipid) kinases (Table 5). Cellular assays also confirmed good
selectivity ratios versus the structurally related PIKKs and PI3 kinases (Table 6). The weak activities in
CSF1R (pIC50 = 5.5) and TTK (pIC50 = 5.3) biochemical assays had been significantly reduced from
compounds 1 and 4, and the binding mode in PI3Kγ was confirmed as placing the optimized
triazolopyridine amine pointing “into” the pocket (amine NH hydrogen bonded to Glu880 residue) as
shown in Figure 2a. We assumed this was likely to represent the binding mode for DNA-PKcs (see Figure
2b), based on sequence homology and it proved to be a better model for explaining SAR such as the
importance of the hydrogen bond acceptor in the para position and the “magic methyl” as described
earlier, and depicted in Figure 2c and 2d. To test broader selectivity, compound 16 was also screened in
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a diverse panel of 195 distinct molecular targets (receptors, ion channels, transporters and enzymes), and
no targets had activity within 100-fold of the primary target potency.34
Table 5. Compound 16 was tested in a diverse panel of 397 kinases at Thermofisher. Only PI3 kinases
had >50% inhibition at 1µM, which were followed up with fluorescence resonance energy transfer
(FRET) assay dose response IC50 data shown, all generated at Thermofisher including the DNA-PK assay
which gave a very similar IC50 value to the AstraZeneca generated data shown previously (0.6 nM).
Kinase
[ATP] (µM) KM (µM) IC50 (nM)a Selectivity ratio
DNA-PKcs
25
4-10
25
0.7
-
PI3Kα (p110α/p85α) 25
PI3Kβ (p110β/p85α) 150
PI3Kδ (p110δ/p85α) 75
100
1200
760
52
138x
1660x
1050x
73x
166
80
PI3Kγ (p110γ)
25
26
a Geometric mean, n≥3. pIC50 SEM values were all <0.1.
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Table 6. Cell selectivity of 16 versus structurally related PIKKs and PI3 kinases.
1
2
3
Kinase
Assay (cell line, endpoint)
IC50 (µM)a Selectivity ratio
4
5
6
7
8
9
DNA-PKcs
ATM
A549, pDNA-PKcs S2056
HT29, pATM S1981
HT29, pCHK1 S345
0.091
17.9
>29
-
197x
>300x
>300x
>90x
156x
>300x
>300x
15x
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ATR
mTOR/PI3Kα MDA-MB-468, pAKT S473 >30
PDK1
PI3Kα
PI3Kβ
PI3Kδ
PI3Kγ
BT474c, pAKT T208
BT474, pAKT T308
>8.3
14.2
MDA-MB-468, pAKT T308 >30
JEKO-1, pAKT Thr308
RAW-264, pAKT Thr308
>30
1.37
a Geometric mean, n≥4. pIC50 SEM values (for in range data) were <0.1, apart from PI3Kγ where SEM=0.17.
Figure 2. (a) Crystal structure of 16 with PI3Kγ (PDB 6T3C), and (b) a modelled binding mode into a
homology model of DNA-PKcs based on the PI3Kγ crystal structure. The key protein residues that differ
between PI3Kγ and DNA-PKcs in the binding pocket are shown in dark green sticks. Close up views of
the DNA-PKcs homology model are shown to illustrate the predicted binding mode with (c) the
triazolopyridine hydrogen bond acceptor and (d) the “magic methyl”.
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Journal of Medicinal Chemistry
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Chemistry
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A typical route used to explore the structure-activity relationship is shown in Scheme 1. Typically, the
ribose pocket group (tetrahydropyran in this case) was defined early in the synthesis by addition of the
corresponding amine to the dichloropyrimidine core 25, followed by saponification to form acid 26. The
bicyclic core was formed by a Curtius rearrangement and intramolecular addition of the amine to form
the cyclic urea, which could be methylated to form 27. Installation of the aniline group (in this case
aromatic amine 24) could be performed with a Buchwald-Hartwig coupling on the chloropyrimidine core
to synthesize the final product 16. Due to the need for an ortho methyl on the aromatic amine for potency,
many of the aromatic amines were not commercially available and had to be synthesized de novo. An
example is shown for compound 24, where the triazolopyridine ring is formed by intramolecular
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cyclisation of 22, where the pyridine nitrogen cyclizes onto a hydroxylated amidine in the presence of
1
2
3
trifluoroacetic anhydride.
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6
7
8
Scheme 1. Representative synthetic route for compound 16.a
9
H
N
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16
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E
NH2
N
N
N
N
N
i, ii
iii
iv
OH
N
N
N
N
O2N
H2N
O2N
O2N
21
22
23
24
O
O
O
O
Cl
N
O
N
O
v, vi
vii, viii
ix
N
N
O
HN
N
O
N
N
N
N
N
HO
N
N
Cl
N
H
N
N
Cl
N
27
Cl
25
26
16
a
Reagents and conditions: (i) DMFDMA, toluene, 99%. (ii) NH2OH.HCl, MeOH, 94%. (iii) TFAA, THF, 32%. (iv) Pd/C,
NH4HCO2, EtOH, 91%. (v) K2CO3, tetrahydro-2H-pyran-4-amine hydrochloride, MeCN, 73%. (vi) LiOH, THF, H2O, 92%.
(vii) DPPA, NEt3, DMA, 70%. (viii) MeI, NaOH, H2O, THF, 69%. (ix) 24, Brettphos Pd precat G3, Cs2CO3, 1,4-dioxane,
54%.
Preclinical characterization of 16 with cancer cell lines
Compound 16 was progressed into a range of in vitro and in vivo xenograft experiments to ascertain
whether the compound had antiproliferative activity in combination with DSB inducing agents. Data from
these studies have been reported recently.35 We confirmed, as expected, compound 16 was a potent
sensitizer of ionizing radiation and combined effectively with doxorubicin, both of which are known to
cause DSBs. In xenograft and patient-derived xenograft (PDX) models these combinations provided
regressions as measured by overall reduction in mean tumor volume. We also observed some single agent
efficacy, which had not been previously reported for selective DNA-PK inhibitors, in both ATM deficient
and ATM wild type models. We also demonstrated that compound 16 can cause sustained tumor
regression in combination with a PARP inhibitor (olaparib) in some models. The combination with
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Journal of Medicinal Chemistry
olaparib was highly efficacious in an ATM knockout (KO) FaDu xenograft model, where 11/11 mice had
no measurable tumor 150 days after the combination treatment had been stopped.35
1
2
3
4
5
6
7
8
9
In order to gain additional understanding of the compound in combination with olaparib we examined
q.d. dosing schedules (Figure 3, data not previously reported). We found that 50 mg/kg q.d. of 16 was
sufficient to give significant efficacy in combination with 100 mg/kg q.d. dose of olaparib. Increasing the
dose to 100 mg/kg q.d. of 16 in combination with the same dose of olaparib gave additional efficacy,
where we observed robust regressions during drug treatment and only slow tumor re-growth post cessation
of dosing. 100 mg/kg of 16 also caused significant target engagement as measured by pharmacodynamic
modulation of biomarkers pDNA-PKcs (S2056), pRPA32 (S4/8) and γH2AX (Figure 4a), where the free
drug concentration in plasma at 2 hours (Cmax) greatly exceeded the A549 cell IC50 in all 5 mice (geometric
mean = 17 µM, range 8.9 - 26 µM). Pharmacokinetics of the 100 mg/kg dose (Figure 4b) provides >1 µM
free concentrations of drug in plasma for >10 hours in SCID mice. In this particular efficacy experiment,
we estimate from data shown (Figure 4b for PK and Table 6 for cell potency) that compound 16 has
delivered prolonged cover (>12 hours) over pDNA-PK cell IC50, whilst only transiently covering the cell
IC50 for possible off-targets ATM, PI3Kα and PI3Kγ.
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Figure 3. In an ATM KO FaDu model 16 dosed 100 mg/kg q.d. gives tumor regression when combined
with olaparib, with slow re-growth observed post cessation of treatment. Tumor start size 0.13±0.01
cm3. Tumor volume shown is the geometrical mean relative to tumor start size on log scale. Error bars =
SEM, group size n=4-9 of severe combined immunodeficient (SCID) mice.
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1
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17.0
Vehicle
Olaparib 100 mg/kg qd
Compound 16 100mg/kg qd
5
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7
8
Compound 16 50mg/kg qd + Olaparib 100 mg/kg qd
Compound 16 100mg/kg qd + Olaparib 100 mg/kg qd
14.0
12.0
10.0
8.0
9
Regrowth
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6.0
4.0
3.0
2.0
1.0
0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80
Days of Treatment
po dosing
Figure 4. (a) Pharmacodynamic modulation of biomarkers pDNA-PKcs, pRPA32 and γH2AX in the
FaDu ATM KO murine xenograft model, measured 2 h post final dose after 21 days of 100 mg/kg q.d.
treatment with compound 16, each group has geometric mean ± SEM from n=5 SCID mice. (b)
Associated free plasma drug exposure at steady-state following 100 mg/kg q.d. dosing, geometric mean
± SEM from n=3 SCID mice.
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Journal of Medicinal Chemistry
a
1
2
3
4
5
6
350
250
150
150
pDNAPKcs Ser2056
pRPA32 Ser4/8
H2AX
7
8
9
100
50
0
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16
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20
p = 0.001
p = 0.001
p = 0.03
Vehicle
Compound 16 100 mg/kg
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b
Conclusions
A number of preclinical and clinical molecules have been described that inhibit DNA-PKcs with varying
levels of selectivity versus the structurally related PI3 kinases and PIKKs, from over two decades of active
research. Historically, identifying a DNA-PKcs inhibitor that combined good selectivity with good
physical and pharmacokinetic properties has been challenging. More recently two DNA-PKcs inhibitors
have entered clinical trials: VX-984 (Vertex, now licensed to Merck KGaA as M9831) and peposertib
(also known as nedisertib and M3814, also Merck KGaA).10 At the time of writing, peposertib in particular
has been actively developed, with combinations announced on www.clinicaltrials.gov that combine
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peposertib with chemotherapy, irradiation, immune checkpoint inhibition and triplet combinations
thereof.
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5
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8
9
At the outset of our program we were mindful that a DNA-PKcs inhibitor could be used with a variety of
combination partners, including DSB inducers and inhibitors of other key components of the DDR. With
multiple potential combination partners, as well as the possibility of use as monotherapy, it was important
to identify a DNA-PKcs inhibitor 16 that combines excellent kinase selectivity and pharmacokinetic
properties, with a low predicted risk for drug-drug interactions. The kinase selectivity of compound 16 is
impressive, with no significant off-targets in the protein kinome, and only weak activity versus PI3Kα/γ
lipid kinases (Tables 5 and 6). The favorable PK properties also enabled us to establish that compound 16
is efficacious as a single agent in some preclinical models, as well as demonstrating regressions in
preclinical models, by combining with either PARP inhibition (olaparib) or DSB inducers (irradiation or
doxorubicin). These data support progression of compound 16 (AZD7648) into clinical studies, which are
due to initiate in 2019 (NCT03907969).
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Experimental Section
General synthetic protocols. Flash column chromatography (FCC) was performed on Merck
Kieselgel silica (Art. 9385) or on reversed phase silica (Fluka silica gel 90 C18) or on Silicycle cartridges
(40-63 μm silica, 4-330 g) or on Grace resolv cartridges (4-120 g) or on RediSep Rf 1.5 Flash columns or
on RediSep Rf high performance Gold Flash columns (150-415 g weight) or on RediSep Rf Gold C18
reversed-phase columns (20-40 μm silica) either manually or automated using an Isco CombiFlash
Companion system or similar system. Preparative reverse phase HPLC was performed on C18 reversed-
phase silica typically using a Waters XSelect CSH C18 column (5 μm silica, 30 mm diameter, 100 mm
length) using decreasingly polar mixtures as eluent. Analytical UPLC was in general performed with
reverse-phase C18 silica, detection by Electrospray Mass Spectrometry and by UV absorbance recording
a wavelength range of 220-320 nm. Microwave reactions were performed using either Biotage Initiator,
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Journal of Medicinal Chemistry
Personal Chemistry Emrys Optimizer, Personal Chemistry Smithcreator or CEM Explorer. The purities
of compounds for biological testing were assessed by NMR and HPLC to be ≥95%. The synthetic
protocols for representative example compound 16 are included below; protocols for all other examples
are in supporting information.
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(E)-N,N-dimethyl-N'-(4-methyl-5-nitropyridin-2-yl)formimidamide.
1,1-Dimethoxy-N,N-
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dimethylmethanamine (DMFDMA) (26.0 mL, 196 mmol) was added to 4-methyl-5-nitropyridin-2-amine
21 (10.0 g, 65.3 mmol) in toluene (100 mL) at room temperature (RT). The reaction mixture was heated
at reflux for 2 hours and the reaction mixture was allowed to cool to RT. The reaction mixture was
concentrated to afford the title compound (13.5 g, 99%) as a yellow solid; 1H NMR (400 MHz, DMSO-
d6) δ 8.88 (s, 1H), 8.69 (s, 1H), 6.84–6.79 (m, 1H), 3.17 (s, 3H), 3.06 (d, J=0.6 Hz, 3H), 2.53 (d, J=0.7
13
Hz, 3H); C NMR (126 MHz, DMSO-d6) δ 165.5, 157.8, 146.8, 145.1, 140.2, 119.8, 41.1, 35.1, 20.7;
HRMS (m/z): MH+ calculated for C9H13N4O2 209.1039; found 209.1034.
(E)-N-hydroxy-N'-(4-methyl-5-nitropyridin-2-yl)formimidamide
(22).
Hydroxylamine
hydrochloride (9.01 g, 130 mmol) was added to (E)-N,N-dimethyl-N'-(4-methyl-5-nitropyridin-2-
yl)formimidamide (13.5 g, 64.8 mmol) in MeOH (100 mL) at RT. The reaction mixture was heated at
reflux for 1 hour and then allowed to cool to RT. The reaction mixture was partitioned between EtOAc
(200 mL) and water (100 mL). The organic layer was isolated and washed with saturated brine (50 mL),
passed through phase-separating filter paper and concentrated to afford the title compound (11.9 g, 94%)
as a yellow solid; 1H NMR (400 MHz, DMSO-d6) δ 10.53 (s, 1H), 10.10 (d, J=8.7 Hz, 1H), 8.89 (s, 1H),
7.89 (d, J=9.0 Hz, 1H), 7.06 (s, 1H), 2.52 (s, 3H); 13C NMR (126 MHz, DMSO-d6) δ 155.6, 147.0, 145.6,
139.8, 135.0, 112.4, 21.2; HRMS (m/z): MH+ calculated for C7H9N4O3 197.0675; found 197.0670.
7-Methyl-6-nitro-[1,2,4]triazolo[1,5-a]pyridine (23). 2,2,2-Trifluoroacetic anhydride
(10.1 mL, 72.8 mmol) was added to (E)-N-hydroxy-N'-(4-methyl-5-nitropyridin-2-yl)formimidamide 22
(11.9 g, 60.7 mmol) in THF (100 mL) at 0°C. The reaction mixture was stirred at RT for 18 hours and
then concentrated. The resulting crude mixture was purified by FCC, eluting with 0–100% EtOAc in
heptane, to afford an impure pale-orange solid. This solid was recrystallized from heptane:EtOAc, filtered
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and dried in vacuo, then taken up in EtOAc (100 mL), washed with 0.1 M aqueous HCl (50 mL), water
(50 mL) and saturated brine (50 mL). The organic layer was passed through phase-separating filter paper
and concentrated in vacuo to afford the title compound (3.42 g, 32%); 1H NMR (400 MHz, DMSO-d6) δ
9.97 (s, 1H), 8.73 (s, 1H), 8.01–7.88 (m, 1H), 2.67 (d, J=0.8 Hz, 3H); 13C NMR (126 MHz, DMSO-d6) δ
157.6, 151.2, 140.2, 136.1, 129.7, 117.2, 20.5; HRMS (m/z): MH+ calculated for C7H7N4O2 179.0569;
found 179.0565.
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7-Methyl-[1,2,4]triazolo[1,5-a]pyridin-6-amine (24). Pd/C (10%, wet support; 0.409 g, 3.84
mmol) was added to 7-methyl-6-nitro-[1,2,4]triazolo[1,5-a]pyridine 23 (3.42 g, 19.2 mmol) and
ammonium formate (6.05 g, 96.0 mmol) in ethanol (150 mL) at RT. The reaction mixture was heated at
reflux for 2 hours, then allowed to cool to RT, filtered and concentrated to afford the title compound (2.60
g, 91%) as a pale-brown solid; 1H NMR (400 MHz, DMSO-d6) δ 8.10 (s, 1H), 8.09 (s, 1H), 7.47 (s, 1H),
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5.00 (s, 2H), 2.26 (s, 3H); C NMR (126 MHz, DMSO-d6) δ 152.3, 145.5, 137.9, 133.6, 114.8, 110.1,
18.2; HRMS (m/z): MH+ calculated for C7H9N4 149.0827; found 149.0822.
Ethyl 2-chloro-4-((tetrahydro-2H-pyran-4-yl)amino)pyrimidine-5-carboxylate. Potassium
carbonate (62.5 g, 452 mmol) was added to ethyl 2,4-dichloropyrimidine-5-carboxylate 25 (40 g, 181
mmol) and tetrahydro-2H-pyran-4-amine hydrochloride (24.9 g, 181 mmol) in acetonitrile (1 L). The
reaction mixture was stirred at RT for 16 hours. The precipitate was collected by filtration and washed
with THF (750 mL), and the organic layers were removed under reduced pressure. The crude product was
purified by FCC, elution gradient 0–2% THF in DCM, to afford the title compound (37.7 g, 73%) as a
pale-yellow solid; 1H NMR (400 MHz, DMSO-d6) δ 8.64 (s, 1H), 8.33 (d, J=7.6 Hz, 1H), 4.33 (q, J=7.1
Hz, 2H), 4.20 (dddd, J=14.9, 10.7, 8.4, 4.3 Hz, 1H), 3.86 (dt, J=11.8, 3.7 Hz, 2H), 3.46 (td, J=11.6, 2.3
Hz, 2H), 1.84–1.93 (m, 2H), 1.53–1.65 (m, 2H), 1.32 (t, J=7.1 Hz, 3H); 13C NMR (126 MHz, DMSO-d6)
δ 165.9, 163.1, 160.1, 160.8, 104.5, 66.1, 61.8, 47.1, 32.3, 14.4; HRMS (m/z): MH+ calculated for
C12H17ClN3O3 286.0958; found 286.0948.
2-Chloro-4-((tetrahydro-2H-pyran-4-yl)amino)pyrimidine-5-carboxylic acid (26). A solution
of LiOH (13.1 g, 547 mmol) in water (800 mL) was added to a stirred solution of ethyl 2-chloro-4-
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((tetrahydro-2H-pyran-4-yl)amino)pyrimidine-5-carboxylate (78.2 g, 273 mmol) in THF (800 mL). The
reaction mixture was stirred at RT for 3 hours. The organic layers were removed under reduced pressure.
The reaction mixture was acidified with 2 M aqueous HCl. The precipitate was collected by filtration,
washed with water (500 mL) and dried under vacuum to afford the title compound (66.4 g, 92%) as a
white solid; 1H NMR (400 MHz, DMSO-d6) δ 13.76 (s, 1H), 8.60 (s, 1H), 8.55 (d, J=7.6 Hz, 1H), 4.18
(tdt, J=11.7, 8.3, 4.2 Hz, 1H), 3.85 (dt, J=11.7, 3.6 Hz, 2H), 3.46 (td, J=11.5, 2.2 Hz, 2H), 1.94–1.85 (m,
2H), 1.62–1.50 (m, 2H); 13C NMR (126 MHz, DMSO-d6) δ 167.9, 163.0, 161.4, 161.0, 104.9, 66.1, 46.9,
32.4; HRMS (m/z): MH+ calculated for C10H13ClN3O3 258.0640; found 258.0645.
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2-Chloro-9-(tetrahydro-2H-pyran-4-yl)-7,9-dihydro-8H-purin-8-one. Triethylamine (25.4 g,
251 mmol) was added to 2-chloro-4-((tetrahydro-2H-pyran-4-yl)amino)pyrimidine-5-carboxylic acid 26
(64.8 g, 251 mmol) and diphenylphosphoryl azide (DPPA) (69.2 g, 251 mmol) in DMA (330 mL). The
reaction mixture was stirred at RT for 1 hour and then stirred at 120°C for 16 hours. The reaction mixture
was poured into ice (2 L), and the precipitate was collected by filtration, washed with water (400 mL) and
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dried under vacuum to afford the title compound (44.8 g, 70%) as a white solid; H NMR (400 MHz,
DMSO-d6) δ 11.62 (s, 1H), 8.14 (s, 1H), 4.42 (t, J=12.3 Hz, 1H), 4.03–3.93 (m, 2H), 3.45 (t, J=12.1 Hz,
2H), 2.45 (dd, J=12.8, 4.3 Hz, 2H), 1.69 (d, J=11.6 Hz, 2H); 13C NMR (126 MHz, DMSO-d6) δ 153.0,
152.1, 150.5, 134.5, 121.6, 66.8, 49.6, 29.6; HRMS (m/z): MH+ calculated for C10H12ClN4O2 255.0649;
found 255.0645.
2-Chloro-7-methyl-9-(tetrahydro-2H-pyran-4-yl)-7,9-dihydro-8H-purin-8-one
(27).
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solution of NaOH (31.0 g, 776 mmol) in water (80 mL) was added to a stirred solution of 2-chloro-9-
(tetrahydro-2H-pyran-4-yl)-7,9-dihydro-8H-purin-8-one (39.5 g, 155 mmol) and MeI (48.5 mL, 776
mmol) in THF (720 mL). The reaction mixture was stirred at RT for 16 hours. The organic layer was
removed under reduced pressure. The reaction mixture was diluted with water. The precipitate was
collected by filtration, washed with water (300 mL) and dried under vacuum to afford the title compound
(32.5 g, 69%) as a white solid; 1H NMR (400 MHz, DMSO-d6) δ 8.37 (s, 1H), 4.47 (tt, J=12.2, 4.3 Hz,
1H), 3.98 (dd, J=11.5, 4.6 Hz, 2H), 3.46 (td, J=12.3, 1.8 Hz, 2H), 3.37 (s, 3H), 2.48–2.39 (m, 2H), 1.77–
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1.64 (m, 2H). 13C NMR (126 MHz, DMSO-d6) δ 152.0, 150.4, 150.2, 133.8, 122.7, 66.3, 49.6, 29.2, 27.4;
HRMS (m/z): MH+ calculated for C11H14ClN4O2 269.0805; found 269.0804.
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7-Methyl-2-((7-methyl-[1,2,4]triazolo[1,5-a]pyridin-6-yl)amino)-9-(tetrahydro-2H-pyran-4-
yl)-7,9-dihydro-8H-purin-8-one (16, AZD7648). Caesium carbonate (24.3 g, 74.4 mmol) was added to
2-chloro-7-methyl-9-(tetrahydro-2H-pyran-4-yl)-7,9-dihydro-8H-purin-8-one (10.0 g, 37.2 mmol) and 7-
methyl-[1,2,4]triazolo[1,5-a]pyridin-6-amine (5.51 g, 37.2 mmol) in 1,4-dioxane (200 mL). Brettphos
precat G3 (1.69 g, 1.86 mmol) was added and the resulting suspension was stirred vigorously at 100°C
for 1 hour. A further 1% of catalyst was added and the reaction mixture was stirred for a further 30
minutes. The mixture was cooled to RT and filtered, and the solid was washed with 10% MeOH in DCM
(100 mL). The filtrate was taken and the solvent was removed in vacuo. The resulting crude product was
purified by FCC, eluting with 0–10% MeOH in DCM, then by recrystallization from MeOH and DCM to
afford the title compound (7.59 g, 54%) as a cream solid, mp 251°C; 1H NMR (400 MHz, DMSO-d6) δ
9.11 (s, 1H), 8.65 (s, 1H), , 8.37 (s, 1H), 8.08 (s, 1H), 7.70 (s, 1H), 4.42 (tt, J=12.0, 4.1 Hz, 1H), 3.97 (dd,
J=11.4, 4.2 Hz, 2H), 3.42 (t, J=11.4 Hz, 2H), 3.31 (s, 3H), 2.58–2.52 (m, 2H), 2.40 (s, 3H), 1.72-1.63 (m,
2H). 13C NMR (125.7 MHz, d4-acetic acid) δ 155.7, 154.4, 153.2, 152.6, 147.9, 141.3, 130.4, 129.4, 124.0,
118.5, 115.7, 67.8, 51.6, 30.6, 28.0,18.9; IR (2% w/w dispersion in KBr) 3453, 1729 cm-1; HRMS (m/z):
MH+ calculated for C18H21N8O2 381.1787; found 381.1778.
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Biochemical DNA-PKcs potency. Determined by time resolved FRET measuring a fluorescent
labelled peptide substrate converting to a phosphorylated product. Fluorescently tagged peptide substrate
were purchased from Thermo Fisher Scientific. 12 point half-log compound concentration–response
curves, with a top concentration of 100 μM were generated from 10 mM stocks of compound solubilised
in DMSO using an Echo 555 (Labcyte Inc., Sunnyvale, CA). All assays were performed in white Greiner
1536 well low volume plates (Greiner Bio-One, UK), in a total reaction volume of 3 μL and 1% (v/v)
final DMSO concentration. Enzymes and substrates were added separately to the compound plates and
incubated at room temperature. The kinase reaction was then quenched by the addition of 3 μL of stop
buffer. Stopped assay plates were read using a BMG Pherastar. IC50 values were calculated using a
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Genedata Screener® software (Genedata, Inc., Basel, Switzerland). Full length human DNA-PKcs protein
was purified from HeLa cell extract by ion exchange. Initially DNA-PKcs protein was incubated with
compound for 30 minutes at room temperature in reaction buffer (50 mM Hepes pH 7.5, 0.01% Brij-35,
10 mM MgCl2, 1 mM EGTA, 1 mM DTT, 2 μg/ml Calf Thymus DNA). The reaction was then initiated
by the addition of ATP and fluorescently tagged peptide substrate (Fluorescein-EPPLSQEAFADLWKK,
Thermo Fisher Scientific). The kinase reaction (18 μM ATP, 35 pM DNA-PKcs, 1.6 μM peptide substrate)
was quenched after 40 minutes by the addition of 3 μL of stop buffer (20 mM Tris pH7.5, 0.02% sodium
azide, 0.01% Nonidet-P40, 20 μm EDTA, 4 nM Tb anti-phospho-p53 [Ser15] Antibody. The reaction was
incubated for a further hour and the plates were read on a BMG Pherastar. Data were analysed and IC50
values were calculated using Genedata Screener® software (Genedata, Inc., Basel, Switzerland).
Cellular DNA-PKcs potency; autophosphorylation of DNA-PKcs at S2056 in A549 cell line
stimulated with irradiation by Elisa. A549 cells were plated 15,000 cells/well in a total volume of 40
µL cell media and incubated overnight. 384-well ELISA plates (Greiner 781077 all-black high-bind) were
coated with 0.5 µg/mL DNA-PKcs antibody (Abcam) in phosphate-buffered saline (PBS) overnight at
4°C. Plates were then washed 3x with PBS containing 0.05% Tween-20 (PBS-T) and blocked with 3%
bovine serum albumin (BSA) in PBS for ~2 hours, before a further 3x wash with PBS-T. Test compounds
and reference controls were dosed directly into the cell plates using a Labcyte Echo 555 acoustic
dispenser. Cell plates were then incubated for 1 hour at 37°C before receiving a radiation dose of 8 Gy
(XRAD 160, Precision X-Ray). Cells were incubated for a further 1 hour before removal of cell media.
Lysis buffer (in-house preparation with addition of protease inhibitor cocktail tablets [Roche]), 0.1%
Tween-20, and 0.1% NP40 was dispensed at 25 µL/well and plates were incubated at 4°C for 15–20 min.
Cell lysates (20 µL/well) were transferred to the DNA-PKcs antibody-coated ELISA plates using a CyBio
Felix liquid handling platform, and ELISA plates were incubated at 4°C overnight. The following day,
ELISA plates were washed 3x with PBS-T and dispensed with in-house DNA-PKcs pSer2056 antibody
(0.5 µg/mL in 3% BSA/PBS) at 20 µL/well. Plates were incubated with antibody for 1.5 hours at RT
before 3x wash with PBS-T. Goat anti-rabbit HRP secondary antibody (1:2000 dilution in 3% BSA/PBS)
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was dispensed at 20 µL/well and plates were incubated at RT for 1 hour before 3x wash with PBS-T.
QuantaBlu working substrate solution (Thermo Scientific #15169, prepared according to manufacturer’s
instructions) was dispensed at 20 µL/well and plates were incubated at RT for 1 hour before a further 20
µL/well dispense with QuantaBlu stop solution provided within the kit. The fluorescence intensity of
individual wells was determined using a PerkinElmer EnVision plate reader.
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In vivo studies were conducted in the UK in accordance with UK Home Office legislation, the
Animal Scientific Procedures Act 1986, the Home Office project licences 70/8894 and P0EC1FFDF and
AstraZeneca’s global bioethics policy.
Notes
The authors declare no competing financial interest.
Acknowledgements
The authors would like to acknowledge Jacqueline Fok for generation of cell selectivity data, Ieuan
Roberts for biochemical selectivity data, Alex Harmer for generation and interpretation of hERG data
and Jens Petersen for generation of x-ray structure.
Corresponding Author(s)
E-mail: frederick.goldberg@astrazeneca.com
Abbreviations used
AO, aldehyde oxidase; ATM, ataxia-telangiectasia mutated kinase; ATR, ataxia telangiectasia mutated
and Rad3-related; BCRP, breast cancer resistance protein; CSF1R, colony stimulating factor 1 receptor;
DDR, DNA damage response; DMFDMA, 1,1-Dimethoxy-N,N-dimethylmethanamine; DNA-PK,
DNA-dependent protein kinase; DNA-PKcs, DNA-dependent protein kinase catalytic subunit; DPPA,
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diphenylphosphoryl azide; DSB, double-strand DNA breaks; ER, efflux ratio; fu, fraction unbound;
H2AX, H2A histone family member X; KO, knockout; LLE, ligand lipophilic efficiency; MRP1, multi-
drug resistant protein 1; NHEJ, non-homologous end joining; PARP, poly ADP-ribose polymerase;
PDX, patient-derived xenograft; PIKK, PI3-kinase related protein kinase; RPA32, replication protein A
32 kDa subunit; SCID, severe combined immunodeficient; SEM, standard error of the mean; SGF,
simulated gastric fluid; TTK, dual-specificity protein kinase; XLF, XRCC4-like factor; XRPD, x-ray
powder diffraction; XRCC4, x-ray repair cross-complementing protein 4.
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Supporting Information
The Supporting Information is available free of charge on the ACS Publications website at xxxx.
Statistical measurements (pIC50, SEM, n) for DNA-PKcs potency data. Biochemical selectivity data
generated at Thermofisher with protocol. Protocols for cellular selectivity assays. hERG assay protocol.
X-ray crystallography protocol. Homology model protocol. Metabolism identification of compound 4.
Preparation and characterization for compounds 1-15, 17-20.
For PDB codes 6T2W (CSF1R, compound 4), 6T3B (PI3Kγ, compound 4) and 6T3C (PI3Kγ, compound
16) authors will release the atomic co-ordinates and experimental data upon article publication. For the
homology model (DNA-PK, compound 16) the PDB file is available as part of the supporting information.
Molecular formula strings for the final compounds (CSV).
References
(1)
Hanahan, D.; Weinberg, R. A. Hallmarks of Cancer: The Next Generation. Cell 2011, 144, 646-
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674.
1
2
3
4
5
6
7
8
(2)
(3)
O’Connor, M. J. Targeting the DNA Damage Response in Cancer. Mol. Cell 2015, 60, 547-560.
Pilié, P. G.; Tang, C.; Mills, G. B.; Yap, T. A. State-of-the-Art Strategies for Targeting the DNA
9
Damage Response in Cancer. Nat. Rev. Clin. Oncol. 2019, 16, 81-104.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
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54
55
56
57
58
59
60
(4)
(5)
(6)
Brown, J. S.; O’carrigan, B.; Jackson, S. P.; Yap, T. A. Targeting DNA Repair in Cancer: Beyond
PARP Inhibitors. Cancer Discov. 2017, 7, 20-37.
Minchom, A.; Aversa, C.; Lopez, J. Dancing with the DNA Damage Response: Next-Generation
Anti-Cancer Therapeutic Strategies. Ther. Adv. Med. Oncol. 2018, 10, 1-18.
Chang, H. H. Y.; Pannunzio, N. R.; Adachi, N.; Lieber, M. R. Non-Homologous DNA End Joining
and Alternative Pathways to Double-Strand Break Repair. Nat. Rev. Mol. Cell Biol. 2017, 18, 495-
506.
(7)
(8)
Goodwin, J. F.; Knudsen, K. E. Beyond DNA Repair: DNA-PK Function in Cancer. Cancer
Discov. 2014, 4, 1126-1139.
Stiff, T.; O’driscoll, M.; Rief, N.; Iwabuchi, K.; Löbrich, M.; Jeggo, P. A. ATM and DNA-PK
Function Redundantly to Phosphorylate H2AX after Exposure to Ionizing Radiation. Cancer Res.
2004, 64, 2390-2396.
(9)
Garces, A. E.; Stocks, M. J. Class 1 PI3K Clinical Candidates and Recent Inhibitor Design
Strategies: A Medicinal Chemistry Perspective. J. Med. Chem. 2019, 62, 4815-4850.
(10) Harnor, S. J.; Brennan, A.; Cano, C. Targeting DNA-Dependent Protein Kinase for Cancer
Therapy. ChemMedChem 2017, 12, 895-900.
(11) Blackford, A. N.; Jackson, S. P. ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA
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Damage Response. Mol. Cell 2017, 66, 801-817.
1
2
3
(12) Cano, C.; Saravanan, K.; Bailey, C.; Bardos, J.; Curtin, N. J.; Frigerio, M.; Golding, B. T.;
Hardcastle, I. R.; Hummersone, M. G.; Menear, K. A.; Newell, D. R.; Richardson, C. J.; Shea, K.;
Smith, G. C. M.; Thommes, P.; Ting, A.; Griffin, R. J. 1-Substituted (Dibenzo[b,d]Thiophen-4-
Yl)-2-Morpholino-4H-Chromen-4-Ones Endowed with Dual DNA-PK/PI3-K Inhibitory Activity.
J. Med. Chem. 2013, 56, 6386-6401.
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60
(13) Finlay, M. R. V.; Griffin, R. J. Modulation of DNA Repair by Pharmacological Inhibitors of the
PIKK Protein Kinase Family. Bioorg. Med. Chem. Lett., 2012, 22, 5352-5359.
(14) Rossello, X.; Riquelme, J. A.; He, Z.; Taferner, S.; Vanhaesebroeck, B.; Davidson, S. M.; Yellon,
D. M. The Role of PI3Kα Isoform in Cardioprotection. Basic Res. Cardiol. 2017, 112, 66.
(15) Andrews, D. M.; Jones, C. D.; Simpson, I.; Ward, R. A. 2-Anilinopurin-8-One Derivatives as
TKK/MPS1 Inhibitors and Their Preparation, Pharmaceutical Compositions and Use in the
Treatment of Proliferative Disorders, WO Patent 2009024824(A1), February 26, 2009.
(16) Baretic, D.; Maia de Oliveira, T.; Niess, M.; Wan, P.; Pollard, H.; Johnson, C. M.; Truman, C.;
McCall, E.; Fisher, D.; Williams, R.; Phillips, C. Structural Insights into the Critical DNA Damage
Sensors DNA-PKcs, ATM and ATR. Prog. Biophys. Mol. Biol. 2019, 147, 4-16.
(17) Huggins, D. J.; Sherman, W.; Tidor, B. Rational Approaches to Improving Selectivity in Drug
Design. J. Med. Chem. 2012, 55, 1424-1444.
(18) Nelson, S. D. Metabolic Activation and Drug Toxicity. J. Med. Chem. 1982, 25, 753-765.
(19) Attia, S. M. Deleterious Effects of Reactive Metabolites. Oxidative Medicine and Cellular
Longevity. 2010, 3, 238-253.
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